my lab is struggeling with our Agarose Gel Electrophoresis. Somehow the markers were always well separated over the gel but the DNA bands are stuck far higher than they should run. So if we try to separate digested plasmides/DNA, we get the right numbers and estimately right spacing within the bands but the bands are not running in the right correlation to the markers.

I have the feeling that our electrophoresis chamber is not working properly since separation always requires at least 75min at 130V and 400mA (but you can see a strong bubbeling at the electrode). One test gel run in a chamber of another lab showed nice separation.

So what do you think? Its caused by the buffer? By the chamber? Or by the power supply? Any ideas?

The height of the buffer in the chamber. Though you are putting in a specific voltage and amperage more buffer will increase resistance, and therefore take away from the speed at which your bands run. Looking from the side of the box 0.5-1.0 cm above the cell is usually what I run. Not more. Plus, try to keep it consistent from gel-to-gel.

The initial run speed. Most people ignore this, but it's a very useful trick. If I'm running a 120V gel, I always run it at 90V until the sample is all the way out of the well and into the lane (this is usually ~10 minutes). This way I can be more confident that my samples are running at the same velocity through the well when it counts. Basically, this is allowing your sample more time to snake its way into the pores of the gel, rather than cramming it in.

Clean the electrodes in the box (that interface with buffer) with some diluted acetic acid or soap.